BSDB

The conformational change and the identification of the mechanical clamp for proteins can be derived by looking at the unfolding scenario. A unfolding scenario shows distance d_u at which a given native contact is broken for the last time. Contacts in the scenario diagrams are identified by the sequential distance |j - i|. A contact is said to be broken if the distance between amino acids i and j exceeds 1.5σ_ij. An accumulation of many contacts unfolding events at a value of d_u indicates emergence of a force peak. In such figure the y-axis shows the sequential separation between two amino acids that make a native contact. The x-axis indicates at which displacement of the pulling tip the contact is broken for the last time. Notice that thermal fluctuations may reinstate a broken contact temporarily and that’s why we seek the last, and thus definitive, rupture event.

As an example we show the unfolding diagram for the first chain of protein 1c4p. This protein contains an α helix (196-210), denoted as I, and eight β strands, denoted as A through H, as labelled consecutively from the N to C termini. These β strands form three β sheets: a, b, and c. The a sheet comprises four strands (A, B, G, E), b sheet two ( C, F), and c-sheet also two ( D, H). These letters are indicated on the unfolding scenario figure and show which secondary structures are involved in a contact that is broken at the distance d_u. The data symbols marked by asterisks correspond to contacts which do not involve any secondary structures. The remaining symbols are diversified and have a meaning identified by the letter symbols placed next to them. The force peak at about 140 Å involves a near simultaneous rupture of the contacts which relate to the terminal strands A and G: A+G (meaning between A and G), A+I, G+I (i.e. with the helix) as well as D+H, A+B, E+G, D+G, C+G, and A+C. Breaking these contacts results in destroying the a β-sheet. Later on, the remaining contacts, such as C+F in the b sheet are broken and the helix is the last to unravel.

ICN I J |I-J| Displacement error 1 1 132 131 24.81 0.46 2 1 133 132 23.94 0.90 3 1 136 135 23.87 0.91 4 2 7 5 482.60 2.49 5 2 132 130 27.63 0.07 6 3 7 4 482.59 2.50 7 3 8 5 476.06 0.40 8 3 11 8 468.95 2.68 9 3 129 126 35.54 0.18 10 3 132 129 27.85 0.04 11 3 133 130 27.86 0.04 12 4 7 3 490.15 1.89 13 4 8 4 485.76 4.07 14 5 8 3 493.05 1.64 15 5 9 4 491.88 1.02 16 6 9 3 499.19 1.43 17 6 10 4 491.88 1.03 18 7 10 3 498.38 1.83 19 7 11 4 501.42 0.31 20 7 129 122 43.96 1.95 21 7 132 125 46.68 0.58 22 8 11 3 501.43 0.32 23 8 12 4 484.73 4.32 24 9 12 3 501.25 0.23 25 9 13 4 493.53 3.63 26 10 13 3 495.28 2.76 27 10 14 4 493.54 3.64 28 10 126 116 67.89 1.54 29 11 14 3 499.89 0.46 30 11 15 4 499.96 0.48 31 11 75 64 67.20 1.92 32 11 129 118 66.63 1.60 33 11 130 119 66.62 1.60 34 12 15 3 499.97 0.47 35 12 16 4 499.96 0.48 36 13 16 3 501.47 0.28 37 13 17 4 501.45 0.27 38 14 17 3 516.99 1.58 39 14 18 4 501.45 0.27 40 14 114 100 91.70 0.42 41 14 118 104 93.19 0.30 42 14 121 107 91.18 0.68 43 14 122 108 90.92 0.81 44 14 126 112 88.66 0.03 45 14 130 116 87.75 0.10 46 15 18 3 499.93 0.48 47 15 68 53 89.22 0.20 48 15 71 56 88.68 0.07 49 15 72 57 88.32 0.24 50 15 75 60 88.32 0.24 51 15 110 95 91.68 0.43 52 15 114 99 91.78 0.39 53 17 118 101 102.69 0.66 54 17 121 104 102.55 0.72 55 18 23 5 456.51 5.98 56 18 68 50 102.46 0.74 57 18 114 96 102.47 0.73 58 18 118 100 106.64 0.81 59 19 22 3 497.24 0.04 60 19 23 4 474.49 7.99 61 20 23 3 500.68 1.76 62 20 24 4 467.42 4.45 63 20 65 45 104.50 0.26 64 20 68 48 104.49 0.26 65 20 69 49 102.49 0.74 66 21 25 4 483.34 3.63 67 21 65 44 107.41 1.41 68 22 26 4 488.06 2.74 69 22 117 95 133.35 0.48 70 23 26 3 497.04 1.75 71 23 27 4 478.94 0.20 72 23 68 45 119.28 0.53 73 23 110 87 122.90 0.61 74 23 113 90 125.39 0.43 75 23 114 91 128.87 2.17 76 23 117 94 133.55 0.38 77 24 27 3 497.05 1.75 78 24 28 4 497.05 1.75 79 24 64 40 119.29 0.53 80 24 68 44 119.28 0.53 81 25 28 3 497.25 1.85 82 25 29 4 497.04 1.75 83 25 61 36 123.36 0.47 84 25 64 39 119.39 0.56 85 26 29 3 496.13 2.41 86 26 30 4 485.01 3.14 87 26 55 29 141.90 0.96 88 26 113 87 136.49 0.87 89 26 117 91 141.57 0.98 90 27 30 3 500.09 0.43 91 27 31 4 494.32 2.44 92 27 109 82 134.01 0.34 93 27 110 83 134.00 0.33 94 27 113 86 138.22 0.01 95 28 31 3 493.97 2.62 96 28 32 4 496.05 1.58 97 28 42 14 141.90 0.46 98 28 60 32 141.91 0.96 99 28 64 36 135.14 0.21 100 29 32 3 498.40 2.75 101 29 33 4 481.07 1.10 102 29 54 25 142.47 0.74 103 29 55 26 142.50 0.75 104 29 60 31 141.95 0.98 105 30 33 3 491.81 3.71 106 30 34 4 481.04 1.12 107 30 109 79 142.04 0.91 108 30 112 82 142.47 0.78 109 30 113 83 142.46 0.77 110 31 34 3 503.55 4.02 111 31 35 4 461.62 7.73 112 31 38 7 293.88 1.66 113 31 105 74 142.04 0.91 114 31 106 75 142.03 0.92 115 31 109 78 142.42 0.77 116 32 36 4 407.32 9.71 117 32 38 6 288.31 1.13 118 32 39 7 206.37 31.02 119 32 42 10 202.85 29.30 120 32 48 16 142.70 0.79 121 32 54 22 142.66 0.77 122 32 60 28 142.65 0.77 123 33 51 18 142.69 0.76 124 33 54 21 142.66 0.77 125 35 38 3 507.87 2.08 126 35 105 70 142.10 0.89 127 35 109 74 142.50 0.78 128 36 39 3 513.74 0.72 129 37 40 3 521.74 0.07 130 37 102 65 142.21 0.91 131 37 105 68 142.56 0.77 132 38 41 3 520.27 0.57 133 38 42 4 508.01 2.04 134 38 102 64 142.15 0.91 135 39 42 3 508.01 2.04 136 39 43 4 485.75 3.69 137 39 48 9 143.12 0.68 138 40 43 3 507.86 2.12 139 40 99 59 142.46 0.80 140 41 96 55 142.10 0.82 141 41 97 56 142.19 0.86 142 41 98 57 142.24 0.89 143 41 99 58 142.46 0.80 144 41 102 61 142.59 0.76 145 42 45 3 502.10 0.77 146 42 48 6 330.19 6.82 147 42 63 21 143.05 0.70 148 43 46 3 503.85 0.11 149 45 48 3 629.21 1.81 150 45 57 12 143.41 0.74 151 45 59 14 143.28 0.70 152 45 60 15 143.28 0.70 153 45 63 18 143.27 0.70 154 46 57 11 143.71 0.60 155 47 53 6 361.67 25.37 156 47 57 10 209.07 31.98 157 48 53 5 400.45 5.98 158 48 54 6 294.07 8.44 159 48 57 9 274.20 0.58 160 48 60 12 209.09 31.98 161 49 53 4 474.45 1.86 162 50 53 3 486.93 3.09 163 50 54 4 481.98 1.90 164 51 54 3 498.87 7.16 165 51 55 4 481.96 1.90 166 52 55 3 507.84 2.68 167 52 56 4 479.42 0.64 168 53 56 3 508.00 2.59 169 53 57 4 479.38 0.65 170 54 57 3 496.88 1.44 171 54 60 6 440.86 10.05 172 55 61 6 468.26 4.83 173 56 61 5 484.36 6.12 174 57 60 3 499.50 1.45 175 57 61 4 491.75 2.43 176 58 61 3 491.75 2.43 177 58 62 4 491.75 2.43 178 59 62 3 498.66 2.04 179 59 63 4 493.29 1.66 180 60 63 3 499.22 1.85 181 60 64 4 493.08 1.21 182 61 64 3 499.25 1.85 183 61 65 4 499.25 1.84 184 62 65 3 499.25 1.84 185 62 66 4 499.25 1.84 186 63 66 3 499.25 1.85 187 63 67 4 489.22 3.17 188 64 67 3 493.09 1.24 189 64 68 4 493.09 1.24 190 65 68 3 502.44 3.44 191 65 69 4 493.37 1.39 192 66 69 3 507.11 1.10 193 66 70 4 502.74 3.29 194 67 70 3 505.68 1.82 195 67 71 4 490.88 2.64 196 67 106 39 169.50 3.56 197 68 71 3 507.12 1.10 198 68 72 4 502.74 3.29 199 68 110 42 182.68 3.62 200 69 72 3 505.68 1.82 201 69 73 4 484.37 0.56 202 70 73 3 505.31 1.70 203 70 74 4 479.41 0.94 204 70 85 15 178.21 0.85 205 70 88 18 169.94 3.28 206 71 74 3 479.39 0.93 207 71 75 4 496.15 0.43 208 71 85 14 195.03 7.28 209 71 130 59 236.03 8.10 210 71 133 62 215.06 6.45 211 71 134 63 195.03 7.27 212 71 137 66 178.47 0.96 213 72 75 3 496.16 0.43 214 72 76 4 496.16 0.43 215 73 76 3 500.55 1.70 216 73 77 4 496.17 0.43 217 73 84 11 238.73 14.55 218 74 77 3 496.24 0.46 219 74 78 4 496.15 0.43 220 74 81 7 290.37 0.04 221 74 84 10 271.18 9.62 222 74 85 11 238.71 14.55 223 75 78 3 505.59 0.35 224 75 133 58 243.57 4.37 225 77 80 3 500.23 0.83 226 77 81 4 467.15 0.43 227 77 84 7 318.06 4.90 228 78 81 3 503.65 3.24 229 78 133 55 249.39 3.90 230 80 83 3 490.06 2.22 231 80 84 4 475.97 4.92 232 81 84 3 486.38 4.86 233 81 85 4 475.96 4.92 234 81 136 55 249.67 3.79 235 81 137 56 249.67 3.79 236 81 140 59 249.56 3.85 237 82 85 3 502.30 3.38 238 82 86 4 463.59 8.04 239 82 140 58 249.57 3.85 240 83 86 3 494.12 1.20 241 85 88 3 489.40 1.28 242 85 89 4 483.16 1.56 243 85 137 52 257.15 4.17 244 85 140 55 255.78 3.55 245 85 141 56 255.58 3.46 246 86 89 3 489.49 0.45 247 86 90 4 485.20 2.58 248 87 90 3 497.31 2.67 249 87 91 4 484.34 0.98 250 88 91 3 496.08 3.29 251 88 92 4 483.07 1.60 252 88 141 53 257.45 4.19 253 89 92 3 507.77 5.80 254 89 93 4 483.00 1.59 255 89 140 51 257.46 4.19 256 89 141 52 257.45 4.19 257 89 143 54 257.44 4.19 258 89 144 55 257.32 4.17 259 90 94 4 425.29 30.39 260 90 95 5 425.29 30.39 261 90 144 54 257.41 4.17 262 91 95 4 366.21 9.70 263 91 96 5 338.96 23.32 264 92 96 4 325.59 16.64 265 92 97 5 325.56 16.64 266 92 98 6 319.18 19.66 267 92 103 11 290.91 6.44 268 92 141 49 257.68 4.17 269 93 97 4 325.50 16.63 270 93 141 48 257.75 4.18 271 93 142 49 257.50 4.20 272 93 144 51 257.46 4.19 273 93 145 52 257.44 4.19 274 94 97 3 508.73 0.69 275 94 144 50 257.46 4.19 276 97 145 48 257.67 4.16 277 98 102 4 506.47 0.55 278 98 103 5 506.46 0.54 279 98 145 47 257.83 4.16 280 99 102 3 513.47 2.94 281 99 103 4 506.69 0.44 282 100 103 3 508.40 0.41 283 100 104 4 506.69 0.44 284 100 142 42 257.95 4.16 285 100 145 45 257.91 4.13 286 101 104 3 506.69 0.44 287 101 105 4 506.69 0.44 288 102 105 3 501.65 2.92 289 102 106 4 493.10 2.64 290 103 106 3 497.52 2.87 291 103 107 4 485.55 1.13 292 103 138 35 258.16 4.13 293 103 141 38 258.16 4.13 294 103 142 39 258.12 4.13 295 104 107 3 497.55 4.74 296 104 108 4 489.50 1.26 297 105 108 3 490.05 0.99 298 105 109 4 489.51 1.26 299 106 109 3 499.64 3.11 300 106 110 4 489.49 1.27 301 107 110 3 504.05 3.08 302 107 111 4 489.48 1.96 303 107 134 27 258.38 4.17 304 108 111 3 499.35 2.96 305 108 112 4 489.48 1.97 306 109 112 3 493.20 2.23 307 109 113 4 486.49 0.48 308 110 113 3 490.37 0.81 309 110 114 4 487.42 0.01 310 110 134 24 259.66 4.32 311 111 114 3 500.69 4.29 312 111 115 4 486.29 0.58 313 111 122 11 261.52 4.28 314 111 127 16 260.58 4.27 315 111 130 19 260.57 4.26 316 111 131 20 260.55 4.26 317 111 134 23 260.42 4.21 318 112 115 3 500.69 4.29 319 112 116 4 487.72 1.29 320 113 116 3 493.79 0.25 321 113 117 4 490.86 1.72 322 114 117 3 489.14 0.51 323 114 118 4 486.25 0.58 324 114 122 8 288.65 17.84 325 114 130 16 260.67 4.25 326 115 119 4 467.38 8.81 327 115 122 7 261.53 4.29 328 116 119 3 501.59 1.11 329 118 121 3 503.37 1.68 330 118 122 4 485.79 1.39 331 119 122 3 505.35 0.14 332 120 123 3 538.99 2.96 333 121 126 5 471.63 5.41 334 122 126 4 471.64 5.41 335 122 127 5 455.08 2.88 336 122 130 8 454.74 2.79 337 123 126 3 491.92 1.11 338 123 127 4 473.49 4.50 339 124 127 3 493.40 1.85 340 124 128 4 490.43 0.94 341 125 128 3 492.03 0.14 342 125 129 4 491.94 0.18 343 126 129 3 503.22 4.80 344 126 130 4 491.95 0.18 345 127 130 3 501.24 0.58 346 127 131 4 492.81 0.61 347 128 131 3 500.06 0.79 348 128 132 4 492.84 0.62 349 129 132 3 495.90 1.55 350 129 133 4 492.84 0.62 351 130 133 3 502.69 2.31 352 130 134 4 490.22 1.93 353 131 134 3 496.10 1.00 354 131 135 4 496.09 1.00 355 132 135 3 498.48 0.20 356 132 136 4 483.06 0.57 357 133 136 3 500.75 0.94 358 133 137 4 483.33 0.43 359 134 137 3 499.59 1.52 360 134 138 4 483.32 0.44 361 135 138 3 499.78 1.42 362 135 139 4 483.04 0.58 363 136 139 3 490.97 4.55 364 136 140 4 488.68 2.54 365 137 140 3 494.50 1.60 366 137 141 4 488.86 2.52 367 138 141 3 496.93 1.52 368 138 142 4 488.86 2.52 369 139 142 3 501.81 0.64 370 139 143 4 488.74 2.58 371 140 143 3 498.49 2.30 372 142 145 3 504.11 1.21 373 143 146 3 515.04 4.03